Investigating the North American Crepis (Asteraceae) agamic complex for evidence of homoploid hybridization

Despite the classic place that the North American Crepis (Asteraceae) agamic complex holds in evolutionary literature, few of the hypotheses about the group presented by Babcock and Stebbins 1938 monograph have been tested. In particular, they hypothesized that the seven sexual diploids had strong interfertility barriers that prevented the formation of diploid hybrids. Here I present an analysis of two previously unrecognized diploid morphotypes, which belong to an unresolved clade with Crepis pleurocarpa and Crepis occidentalis based on plastid DNA variation. Morphological traits suggest that both morphotypes may be the product of diploid x diploid hybridization. I gathered nuclear SNP markers using genotyping by sequencing to assess the origins of these two lineages. I constructed a de novo assembly of the nuclear genome of Crepis monticola to serve as a reference for SNP discovery. Analysis of contig length,number, and coverage indicate that the nuclear genome of Crepis is highly repetitive and shares features in common with other plant genomes that make angiosperm genomes challenging to work with. This complexity, as well as technical challenges likely due to partial enzymatic digestion of genomic DNA during GBS library preparation, resulted in only 19 SNPs passing the quality filters. Nonetheless, these 19 markers were used to provide a preliminary assessment of the origins of novel morphotypes. A signal of mixed ancestry was found for one of these morphotypes with the majority of their genome being distinct from both C. occidentalis subsp. occidentalis and C. pleurocarpa. The second morphotype is of non-mixed ancestry most closely resembling Crepis occidentalis. In a separate study, I provide a draft assembly of the Crepis monticola chloroplast genome. I show that gene order and content are unchanged from other members of Asteraceae with the exception of the rpl16 gene, which retains an intron that is reported as lost multiple times in Asteraceae. Results of a preliminary data analysis detailing the presence or absence of the first exon of rpl16 in published Asteraceae plastome sequences indicates that most of these supposed losses are errors, pointing to the need for careful examination of plastome assemblies gathered from databases.Science, Faculty ofBotany, Department ofGraduat